If you just copy and paste the manifest file from your Android Studio build directory to the Unity Android plugin directory you will see compile and build errors. It appears in Unity 4.6 that if you place a manifest file in the Android plugin directory it overrides the Unity created manifest file for the entire app.

The best solution is to find the Unity generated manifest file, copy it to a temp directory and modify by adding any permissions you need (in my case bluetoth related), then add to the Android plugins folder – Unity will use this manifest file as the default and all will be well.